Summary The thymus produces new T lymphocytes throughout life to maintain peripheral homeostasis and immune function. Unlike other tissues that undergo steady-state differentiation, the thymus contains no self-renewing stem or progenitor cells, and instead depends on constant recruitment of marrow-derived progenitors that circulate in the blood. The earliest intrathymic progenitors are multi-potent, but upon entering the thymus they lose other lineage potential and differentiate into T lineage cells. In addition, they go through multiple phases of proliferation, and eventually differentiate asymmetrically into multiple, functionally-distinct T lineages. While several of the more important molecular signals for this process have been defined, they are too few to adequately explain the complexity of these processes. To address this, we have used two different approaches to identify other signals that are provided to differentiating T progenitors by the thymic microenvironment. The first utilized a reverse identification strategy, in which receptors expressed on developing lymphocytes were used to predict the existence of thymic microenvironmental signals. Using this approach, we have identified requirements for several novel signals in during thymocyte differentiation. One of these, neuropilin-1 (Nrp1), is discussed in detail here. Nrp1 has a well characterized role in regulating chemorepulsive cell migration in a variety of differentiating tissues. Conditional deletion of Nrp1 in thymocytes leads to a smaller thymus, and a marked reduction in cellularity at the CD4/8-double positive (DP) and single-positive (SP) stages. This is associated with a defect in progenitor migration to the sub-capsular zone (SCZ), where CD4/8-double positive cells are generated. We propose that Nrp1 is required for the migration of early progenitor cells outward to the SCZ, and describe experiments aimed at elucidating the mechanisms of Nrp1 function and the consequences of impairment. In the second approach, we have used laser microdissection and microarray analysis of tissues and lymphoid cells from discrete regions of the thymus to generate a comprehensive map of stromal and lymphoid gene expression. Using this approach, we have identified what genes define each functionally distinct region of the thymus, and what makes each of them unique. We now propose experiments to allow us to further refine this data, to define stromal:lymphoid and stromal:stromal signaling interactions, and to generate region-specific tools that may be used to further probe the functions of these regions.